zalpha (version 0.3.0)

LR: Runs the LR function

Description

Returns the |L||R| value for each SNP location supplied to the function, where |L| and |R| are the number of SNPs to the left and right of the current locus within the given window ws. For more information about the |L||R| diversity statistic, please see Jacobs (2016).

Usage

LR(pos, ws, X = NULL)

Arguments

pos

A numeric vector of SNP locations

ws

The window size which the LR statistic will be calculated over. This should be on the same scale as the pos vector.

X

Optional. Specify a region of the chromosome to calculate LR for in the format c(startposition, endposition). The start position and the end position should be within the extremes of the positions given in the pos vector. If not supplied, the function will calculate LR for every SNP in the pos vector.

Value

A list containing the SNP positions and the LR values for those SNPs

References

Jacobs, G.S., T.J. Sluckin, and T. Kivisild, Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps. Genetics, 2016. 203(4): p. 1807

Examples

# NOT RUN {
## load the snps example dataset
data(snps)
## run LR over all the SNPs with a window size of 3000 bp
LR(snps$bp_positions,3000)
## only return results for SNPs between locations 600 and 1500 bp
LR(snps$bp_positions,3000,X=c(600,1500))

# }